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BALTRON was created as an international squadron to minimise mine hazards, improve the safety of peacetime navigation and help to remediate environmental damage in the territorial waters and economic zones of Estonia, Latvia and Lithuania. International co-operation in the framework of BALTRON and the foreign aid accompanying the project help to speed up the development of the Baltic navies, thereby enhancing the defence capabilities of each state.

BALTRON improves mutual understanding between the navies of the Baltic states and their interoperability and helps to integrate them with the respective NATO units.
Structure and organisation of BALTRON
BALTRON comprises the Joint Staff of the Baltic States and ships of the navies of Estonia, Latvia and Lithuania. Every state allocates 1-2 minehunters to BALTRON. The authorities of the Baltic states annually agree on the allocation of ships, appointment of staff members and specific operations - the annual plan of BALTRON's activity is prepared accordingly.

The ships allocated to BALTRON remain parts of the Baltic navies and therefore the joint squadron is based on the support of the three navies. One ship performs the tasks of a command and support ship. Estonia has allocated facilities at the Tallinn Miinisadam Port for BALTRON on-shore facilities for the shore staff.

BALTRON staff is formed of representatives of the Estonian, Latvian and Estonian navies. The staff positions are rotated between the officers of the three states. This helps to ensure an equal participation of the navies involved in the project, the participants also gain an equal share of experience to be able to act in accordance with the internationally established terms of co-operation. In Spring 1998 the Latvian Navy Captain Ilmars Leshinskis was appointed as the first Commander of BALTRON.